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A list by Merve Tepe 😷💉🇺🇦🕊️☮️

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  4. CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis

    1. Adrian Sven Geissler
    2. Annaleigh Ohrt Fehler
    3. Line Dahl Poulsen
    4. Enrique González-Tortuero
    5. Thomas Beuchert Kallehauge
    6. Ferhat Alkan
    7. Christian Anthon
    8. Stefan Ernst Seemann
    9. Michael Dolberg Rasmussen
    10. Anne Breüner
    11. Carsten Hjort
    12. Jeppe Vinther
    13. Jan Gorodkin
    Appears in 1 listLatest version

  6. Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individual C. elegans neurons

    1. Alec Barrett
    2. Erdem Varol
    3. Alexis Weinreb
    4. Seth R Taylor
    5. Rebecca M McWhirter
    6. Cyril Cros
    7. Berta Vidal
    8. Manasa Basaravaju
    9. Abigail Poff
    10. John A Tipps
    11. Maryam Majeed
    12. Chen Wang
    13. Emily A Bayer
    14. Molly Reilly
    15. Eviatar Yemini
    16. HaoSheng Sun
    17. Oliver Hobert
    18. David M Miller
    19. Marc Hammarlund

    • Curated by eLife

      eLife Assessment

      This valuable paper provides refined gene expression datasets for 52 neuron classes in C. elegans using a new method that takes advantage of the complementary strengths of bulk sequencing of flow-sorted cells and single-cell sequencing. In general, support for the paper's findings is convincing. However, more rigorous consideration of some of the method's statistical assumptions and validation of the predicted gene sets would improve the work.

    Reviewed by eLife

    4 evaluationsAppears in 3 listsLatest version Latest activity

  7. Key features of the genetic architecture and evolution of host-microbe interactions revealed by high-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice

    1. Shauni Doms
    2. Hanna Fokt
    3. Malte Christoph Rühlemann
    4. Cecilia J Chung
    5. Axel Kuenstner
    6. Saleh M Ibrahim
    7. Andre Franke
    8. Leslie M Turner
    9. John F Baines

    • Curated by eLife

      Evaluation Summary:

      The paper uses hybrid mouse lines to estimate the heritability of the microbiome and map variants in the mouse genome that are associated with the composition of the microbiome. The findings are of broad interest to microbiome researchers and improve on knowledge in the field, as they focus on mucosa-associated (rather than fecal) microbiome profiles and report a novel correlation between heritability and cospeciation rates. The results are intriguing, but technical and biological confounders are incompletely addressed in the manuscript's present form, potentially leading to surprisingly high estimates of microbiome trait heritability relative to previous work.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

    Reviewed by eLife

    4 evaluationsAppears in 2 listsLatest version Latest activity

  8. Understanding drivers of phylogenetic clustering and terminal branch lengths distribution in epidemics of Mycobacterium tuberculosis

    1. Fabrizio Menardo

    • Curated by eLife

      Evaluation Summary:

      This is an interesting simulation-based study focusing on the genomic epidemiology of Mycobacterium tuberculosis. The work nicely relates key biological and epidemiological parameters to how M. tuberculosis isolates cluster together, and to the terminal branch lengths in M. tuberculosis phylogenies. These concepts have both been applied to comparative studies of M. tuberculosis success and have often been interpreted as reflecting differences in transmission. The author finds that clustering and terminal branch lengths can also be modified by differences in the latent period, the mutation rate or the sampling fraction. This work will be of broad interest to readers studying tuberculosis epidemiology and transmission modelling.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

    Reviewed by eLife

    3 evaluationsAppears in 2 listsLatest version Latest activity

  10. The evolution of colistin resistance increases bacterial resistance to host antimicrobial peptides and virulence

    1. Pramod K Jangir
    2. Lois Ogunlana
    3. Petra Szili
    4. Marton Czikkely
    5. Liam P Shaw
    6. Emily J Stevens
    7. Yang Yu
    8. Qiue Yang
    9. Yang Wang
    10. Csaba Pál
    11. Timothy R Walsh
    12. Craig R MacLean

    • Curated by eLife

      eLife assessment

      Antimicrobial peptides (AMP) are a class of antibiotics that are inspired by natural components of innate immunity, which raises the specter of bacteria becoming resistant to both. The author this important study test this idea and find compelling evidence that a plasmid that encodes resistance to the AMP colistin also increases resistance to AMPS produced by humans, pigs, and chickens, enables the bacteria to grow better in low levels of AMP, and increases bacterial virulence in an insect model of infection. The study will be of interest to both evolutionary biologists and microbiologists focused on antimicrobial therapy and suggests that the evolution of resistance to these compounds can have collateral effects on immune evasion as well.

    Reviewed by eLife, PREreview

    5 evaluationsAppears in 3 listsLatest version Latest activity

  11. Fast bacterial growth reduces antibiotic accumulation and efficacy

    1. Urszula Łapińska
    2. Margaritis Voliotis
    3. Ka Kiu Lee
    4. Adrian Campey
    5. M Rhia L Stone
    6. Brandon Tuck
    7. Wanida Phetsang
    8. Bing Zhang
    9. Krasimira Tsaneva-Atanasova
    10. Mark AT Blaskovich
    11. Stefano Pagliara

    • Curated by eLife

      Evaluation Summary:

      This manuscript addresses mechanisms by which bacteria are able to survive and evade killing by antibiotics. Using fluorescent versions of antibiotics it studies whether if entry/efflux of the drug itself is a significant contributor to the observed variability of antibiotic activity. This study will be of interest to microbiologists and clinicians for design of better antibiotic therapies.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

    Reviewed by eLife

    4 evaluationsAppears in 2 listsLatest version Latest activity

  12. Amoxicillin-resistant Streptococcus pneumoniae can be resensitized by targeting the mevalonate pathway as indicated by sCRilecs-seq

    1. Liselot Dewachter
    2. Julien Dénéréaz
    3. Xue Liu
    4. Vincent de Bakker
    5. Charlotte Costa
    6. Mara Baldry
    7. Jean-Claude Sirard
    8. Jan-Willem Veening

    • Curated by eLife

      Evaluation Summary:

      Three experts in the field reviewed this manuscript from slightly different perspectives. All three reviewers are generally positive about this interesting, well-presented paper and think that it leads to several advances in the field. However, the reviewers also think changes can be made that would considerably strengthen the current version and its impact. Specific modifications have been requested to improve analysis of the screening data, to discuss hits besides the mevalonate pathway that increase Streptococcus pneumoniae cell length and shape, to clarify some issues about how mevalonate depletion changes pneumococcal cell shape and peptidoglycan synthesis, and to provide more context for clomiphene potentiation of amoxicillin killing of Streptococcus pneumoniae in comparison to previously published results in Staphylococcus aureus.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

    Reviewed by eLife

    5 evaluationsAppears in 2 listsLatest version Latest activity

  13. Humanization of wildlife gut microbiota in urban environments

    1. Brian A Dillard
    2. Albert K Chung
    3. Alex R Gunderson
    4. Shane C Campbell-Staton
    5. Andrew H Moeller

    • Curated by eLife

      Evaluation Summary:

      Urbanization has broad impacts for macroecology but its consequences for wildlife microbial ecology remain unclear. Dillard et al. hypothesize that humans living in an urban setting may transfer their microbes to wildlife with potential adverse effects. They analyze 16S rRNA gene sequencing data from humans, crested anoles, and coyotes, leading to the discovery of multiple bacteria that fit the pattern of urbanization and inter-species transfer.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

    Reviewed by eLife

    5 evaluationsAppears in 2 listsLatest version Latest activity

  14. Metabolic basis for the evolution of a common pathogenic Pseudomonas aeruginosa variant

    1. Dallas L Mould
    2. Mirjana Stevanovic
    3. Alix Ashare
    4. Daniel Schultz
    5. Deborah A Hogan

    • Curated by eLife

      Evaluation Summary:

      This study aimed to identify the genetic foundation favoring selection of lasR mutants in laboratory and clinical isolates from persons with CF. They selected these mutants using a predictable and quantitative framework of evolution experiments and then identified their genetic underpinnings by a a suppressor screen. The role of cbrAB as a key intermediate is important and ties together several reports of nutrient-dependent advantages of lasR like phenylalanine.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

    Reviewed by eLife

    5 evaluationsAppears in 2 listsLatest version Latest activity

  15. An Archaea-specific c-type cytochrome maturation machinery is crucial for methanogenesis in Methanosarcina acetivorans

    1. Dinesh Gupta
    2. Katie E Shalvarjian
    3. Dipti D Nayak

    • Curated by eLife

      Evaluation Summary:

      This paper will be of interest to scientists interested in archaea and the field of bioenergetics. Using a series of elegant experiments the authors show that that archaea have a streamlined and functional cytochrome c biogenesis machinery.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

    Reviewed by eLife

    3 evaluationsAppears in 2 listsLatest version Latest activity

  17. Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules

    1. Yuzuru Itoh
    2. Vivek Singh
    3. Anas Khawaja
    4. Andreas Naschberger
    5. Minh Duc Nguyen
    6. Joanna Rorbach
    7. Alexey Amunts

    • Curated by eLife

      Evaluation Summary:

      As a consequence of the bacterial origin of mitochondria, a range of medically relevant antimicrobials can affect not only bacteria but also human cells. For example, they may inhibit mitochondrial protein synthesis, giving rise to important side-effects during medical treatment, such as hearing loss or renal toxicity in patients treated with aminoglycosides. In this manuscript, the authors present the structure of the human mitochondrial small ribosomal subunit bound to one such antibiotics, streptomycin. This cryoEM-based structural analysis will be of interest to scientists in the infectious disease community as well as those interested in ribosome structural biology. It provides an important advance that could aid future medicinal chemistry efforts to improve the therapeutic potential of streptomycin derivatives.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

    Reviewed by eLife

    4 evaluationsAppears in 2 listsLatest version Latest activity